Starting phenix.real_space_refine on Fri Apr 5 19:47:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/04_2024/8t05_40935_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/04_2024/8t05_40935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/04_2024/8t05_40935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/04_2024/8t05_40935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/04_2024/8t05_40935_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t05_40935/04_2024/8t05_40935_updated.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 22 5.16 5 C 3387 2.51 5 N 798 2.21 5 O 893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "C" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 3.67, per 1000 atoms: 0.72 Number of scatterers: 5104 At special positions: 0 Unit cell: (81.34, 88.81, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 22 16.00 P 2 15.00 O 893 8.00 N 798 7.00 C 3387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 932.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 182 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 186 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 186 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 182 " 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 4 sheets defined 50.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 3 through 27 Proline residue: A 11 - end of helix removed outlier: 3.973A pdb=" N GLY A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 31 through 50 removed outlier: 4.083A pdb=" N LEU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.692A pdb=" N MET A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.738A pdb=" N THR A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 178 through 199 removed outlier: 3.787A pdb=" N SER A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 27 Proline residue: B 11 - end of helix removed outlier: 3.986A pdb=" N GLY B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 17 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 31 through 51 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 64 through 85 removed outlier: 3.628A pdb=" N PHE B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 120 through 140 Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 178 through 198 removed outlier: 3.965A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'C' and resid 17 through 23 Processing sheet with id= B, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.622A pdb=" N ALA C 92 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU C 45 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.560A pdb=" N LYS D 103 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL D 13 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLU D 105 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.533A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 746 1.31 - 1.44: 1499 1.44 - 1.56: 2946 1.56 - 1.69: 14 1.69 - 1.82: 32 Bond restraints: 5237 Sorted by residual: bond pdb=" C GLY C 8 " pdb=" N ALA C 9 " ideal model delta sigma weight residual 1.331 1.409 -0.077 1.30e-02 5.92e+03 3.53e+01 bond pdb=" C25 LBN A 303 " pdb=" O5 LBN A 303 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C25 LBN B 303 " pdb=" O5 LBN B 303 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C34 LBN A 303 " pdb=" O7 LBN A 303 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 303 " pdb=" O7 LBN B 303 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 5232 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.22: 126 106.22 - 113.28: 2774 113.28 - 120.34: 2328 120.34 - 127.40: 1834 127.40 - 134.45: 43 Bond angle restraints: 7105 Sorted by residual: angle pdb=" N PHE C 109 " pdb=" CA PHE C 109 " pdb=" C PHE C 109 " ideal model delta sigma weight residual 111.24 118.85 -7.61 1.38e+00 5.25e-01 3.04e+01 angle pdb=" C GLY A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta sigma weight residual 120.03 125.59 -5.56 1.12e+00 7.97e-01 2.47e+01 angle pdb=" N THR D 94 " pdb=" CA THR D 94 " pdb=" C THR D 94 " ideal model delta sigma weight residual 108.82 117.00 -8.18 1.65e+00 3.67e-01 2.46e+01 angle pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O2 LBN B 303 " ideal model delta sigma weight residual 93.45 108.05 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O1 LBN A 303 " pdb=" P1 LBN A 303 " pdb=" O2 LBN A 303 " ideal model delta sigma weight residual 93.45 107.88 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 7100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.48: 3038 30.48 - 60.96: 92 60.96 - 91.44: 11 91.44 - 121.92: 7 121.92 - 152.40: 4 Dihedral angle restraints: 3152 sinusoidal: 1337 harmonic: 1815 Sorted by residual: dihedral pdb=" CA THR D 94 " pdb=" C THR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 180.00 70.79 109.21 0 5.00e+00 4.00e-02 4.77e+02 dihedral pdb=" CA ALA D 50 " pdb=" C ALA D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA SER B 56 " pdb=" C SER B 56 " pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta harmonic sigma weight residual -180.00 -155.12 -24.88 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 3149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.985: 803 0.985 - 1.969: 0 1.969 - 2.954: 0 2.954 - 3.938: 0 3.938 - 4.923: 2 Chirality restraints: 805 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.56 -4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.92 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" C14 CLR A 302 " pdb=" C13 CLR A 302 " pdb=" C15 CLR A 302 " pdb=" C8 CLR A 302 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 802 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 145 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO B 146 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 13 " -0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO C 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO D 95 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.036 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 71 2.68 - 3.23: 4644 3.23 - 3.79: 7743 3.79 - 4.34: 10751 4.34 - 4.90: 18020 Nonbonded interactions: 41229 Sorted by model distance: nonbonded pdb=" OE1 GLN A 44 " pdb="ZN ZN A 301 " model vdw 2.120 2.230 nonbonded pdb=" OE1 GLN B 44 " pdb="ZN ZN B 301 " model vdw 2.172 2.230 nonbonded pdb=" NH2 ARG D 61 " pdb=" OE2 GLU D 81 " model vdw 2.356 2.520 nonbonded pdb=" NH2 ARG A 108 " pdb=" O PRO A 116 " model vdw 2.413 2.520 nonbonded pdb=" O HIS D 90 " pdb=" ND1 HIS D 90 " model vdw 2.433 2.520 ... (remaining 41224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.710 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.880 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.107 5237 Z= 0.934 Angle : 1.851 14.605 7105 Z= 1.350 Chirality : 0.259 4.923 805 Planarity : 0.006 0.091 848 Dihedral : 16.958 152.400 1982 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.78 % Favored : 93.90 % Rotamer: Outliers : 0.93 % Allowed : 6.16 % Favored : 92.91 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.31), residues: 623 helix: -1.21 (0.25), residues: 313 sheet: -1.44 (0.49), residues: 86 loop : -1.32 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 151 HIS 0.007 0.002 HIS D 90 PHE 0.019 0.002 PHE B 43 TYR 0.043 0.003 TYR D 49 ARG 0.003 0.000 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.545 Fit side-chains REVERT: A 137 GLU cc_start: 0.6864 (tp30) cc_final: 0.6262 (mm-30) REVERT: A 198 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6588 (ttp80) REVERT: B 62 MET cc_start: 0.6309 (mtt) cc_final: 0.6034 (mtm) REVERT: B 184 ILE cc_start: 0.7178 (mm) cc_final: 0.6907 (mt) REVERT: C 10 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7500 (mp0) REVERT: C 28 THR cc_start: 0.8525 (m) cc_final: 0.8298 (t) REVERT: C 32 TYR cc_start: 0.8080 (m-80) cc_final: 0.7604 (m-80) REVERT: C 34 MET cc_start: 0.8066 (mmm) cc_final: 0.7480 (tpt) REVERT: D 30 TYR cc_start: 0.8035 (m-80) cc_final: 0.7673 (m-80) REVERT: D 71 TYR cc_start: 0.7538 (m-80) cc_final: 0.7100 (m-80) REVERT: D 100 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7906 (tp30) outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.2268 time to fit residues: 25.6086 Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 PRO Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain D residue 90 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 95 HIS B 186 HIS D 6 GLN D 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5237 Z= 0.236 Angle : 0.634 7.978 7105 Z= 0.327 Chirality : 0.042 0.187 805 Planarity : 0.005 0.077 848 Dihedral : 16.463 149.245 890 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.24 % Allowed : 10.63 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.34), residues: 623 helix: 1.19 (0.28), residues: 314 sheet: -0.88 (0.47), residues: 117 loop : -0.77 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 47 HIS 0.006 0.001 HIS C 35 PHE 0.017 0.002 PHE D 91 TYR 0.015 0.001 TYR D 49 ARG 0.002 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.429 Fit side-chains REVERT: A 13 ILE cc_start: 0.6902 (mt) cc_final: 0.6679 (mt) REVERT: A 112 GLU cc_start: 0.6191 (tt0) cc_final: 0.5935 (tt0) REVERT: A 137 GLU cc_start: 0.6956 (tp30) cc_final: 0.6395 (mm-30) REVERT: B 27 LYS cc_start: 0.7523 (mmmt) cc_final: 0.6929 (mtmt) REVERT: B 198 ARG cc_start: 0.8224 (ttm170) cc_final: 0.7695 (mtp85) REVERT: C 62 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7997 (mm-40) REVERT: D 4 MET cc_start: 0.7995 (mmm) cc_final: 0.7682 (mtp) REVERT: D 30 TYR cc_start: 0.8163 (m-80) cc_final: 0.7651 (m-80) REVERT: D 90 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.8337 (p-80) REVERT: D 106 ILE cc_start: 0.7630 (pt) cc_final: 0.7411 (mt) outliers start: 12 outliers final: 4 residues processed: 91 average time/residue: 0.2113 time to fit residues: 23.5936 Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5237 Z= 0.163 Angle : 0.553 6.017 7105 Z= 0.277 Chirality : 0.039 0.198 805 Planarity : 0.005 0.075 848 Dihedral : 14.176 135.962 883 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.87 % Allowed : 12.31 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.35), residues: 623 helix: 2.14 (0.29), residues: 308 sheet: -0.58 (0.50), residues: 107 loop : -1.03 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 47 HIS 0.002 0.001 HIS A 48 PHE 0.015 0.001 PHE B 70 TYR 0.013 0.001 TYR D 49 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6985 (mt) cc_final: 0.6753 (mt) REVERT: A 27 LYS cc_start: 0.7881 (tmmt) cc_final: 0.7338 (tptt) REVERT: A 65 LYS cc_start: 0.7841 (mttt) cc_final: 0.6968 (mtpt) REVERT: A 88 ARG cc_start: 0.7469 (mtp-110) cc_final: 0.7236 (mmm-85) REVERT: A 112 GLU cc_start: 0.5560 (tt0) cc_final: 0.5288 (tt0) REVERT: A 137 GLU cc_start: 0.6859 (tp30) cc_final: 0.6079 (mm-30) REVERT: B 27 LYS cc_start: 0.7546 (mmmt) cc_final: 0.6945 (mptt) REVERT: C 32 TYR cc_start: 0.8096 (m-80) cc_final: 0.7830 (m-80) REVERT: D 4 MET cc_start: 0.7958 (mmm) cc_final: 0.7752 (mtp) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.2378 time to fit residues: 25.1554 Evaluate side-chains 82 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5237 Z= 0.324 Angle : 0.638 6.545 7105 Z= 0.324 Chirality : 0.043 0.198 805 Planarity : 0.005 0.083 848 Dihedral : 13.771 156.344 881 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.43 % Allowed : 13.06 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.35), residues: 623 helix: 1.84 (0.28), residues: 313 sheet: -0.80 (0.47), residues: 117 loop : -0.96 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 47 HIS 0.007 0.002 HIS C 35 PHE 0.024 0.002 PHE D 91 TYR 0.020 0.002 TYR D 49 ARG 0.002 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6913 (mt) cc_final: 0.6661 (mt) REVERT: A 88 ARG cc_start: 0.7529 (mtp-110) cc_final: 0.7321 (mmm-85) REVERT: A 112 GLU cc_start: 0.5731 (tt0) cc_final: 0.5471 (tt0) REVERT: A 137 GLU cc_start: 0.7071 (tp30) cc_final: 0.6283 (mm-30) REVERT: B 27 LYS cc_start: 0.7592 (mmmt) cc_final: 0.6976 (mptt) REVERT: D 71 TYR cc_start: 0.7900 (m-80) cc_final: 0.7496 (m-80) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.2841 time to fit residues: 28.0236 Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5237 Z= 0.252 Angle : 0.576 6.567 7105 Z= 0.292 Chirality : 0.041 0.198 805 Planarity : 0.005 0.081 848 Dihedral : 13.014 160.762 881 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.68 % Allowed : 14.93 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.35), residues: 623 helix: 1.98 (0.28), residues: 313 sheet: -0.76 (0.47), residues: 119 loop : -1.13 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.005 0.001 HIS C 35 PHE 0.016 0.001 PHE D 91 TYR 0.017 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6992 (mt) cc_final: 0.6731 (mt) REVERT: A 27 LYS cc_start: 0.7795 (tmmt) cc_final: 0.7290 (tptt) REVERT: A 88 ARG cc_start: 0.7502 (mtp-110) cc_final: 0.7272 (mmm-85) REVERT: A 112 GLU cc_start: 0.5728 (tt0) cc_final: 0.5491 (tt0) REVERT: A 137 GLU cc_start: 0.7036 (tp30) cc_final: 0.6251 (mm-30) REVERT: A 176 TRP cc_start: 0.7276 (t60) cc_final: 0.6945 (t60) REVERT: B 27 LYS cc_start: 0.7588 (mmmt) cc_final: 0.6981 (mptt) REVERT: D 61 ARG cc_start: 0.7589 (ptt90) cc_final: 0.7046 (mtm180) outliers start: 9 outliers final: 9 residues processed: 82 average time/residue: 0.2062 time to fit residues: 21.1137 Evaluate side-chains 84 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5237 Z= 0.161 Angle : 0.516 6.016 7105 Z= 0.260 Chirality : 0.038 0.195 805 Planarity : 0.005 0.076 848 Dihedral : 12.264 159.106 881 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.68 % Allowed : 15.86 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.35), residues: 623 helix: 2.37 (0.29), residues: 312 sheet: -0.37 (0.50), residues: 105 loop : -1.34 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 PHE 0.014 0.001 PHE A 39 TYR 0.013 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7053 (mt) cc_final: 0.6799 (mt) REVERT: A 27 LYS cc_start: 0.7802 (tmmt) cc_final: 0.7294 (tptt) REVERT: A 88 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.7211 (mmm-85) REVERT: A 112 GLU cc_start: 0.5453 (tt0) cc_final: 0.5212 (tt0) REVERT: A 137 GLU cc_start: 0.6906 (tp30) cc_final: 0.6096 (mm-30) REVERT: B 27 LYS cc_start: 0.7523 (mmmt) cc_final: 0.6934 (mptt) REVERT: D 61 ARG cc_start: 0.7485 (ptt90) cc_final: 0.7058 (mtm180) REVERT: D 74 LYS cc_start: 0.7487 (ptmm) cc_final: 0.7138 (ptmm) REVERT: D 81 GLU cc_start: 0.7444 (pm20) cc_final: 0.7215 (pm20) outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 0.2091 time to fit residues: 19.9089 Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5237 Z= 0.205 Angle : 0.540 6.204 7105 Z= 0.272 Chirality : 0.040 0.196 805 Planarity : 0.005 0.079 848 Dihedral : 12.026 165.689 881 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.68 % Allowed : 16.42 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.35), residues: 623 helix: 2.26 (0.28), residues: 318 sheet: -0.30 (0.50), residues: 105 loop : -1.33 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.005 0.001 HIS C 35 PHE 0.014 0.001 PHE D 91 TYR 0.015 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6985 (mt) cc_final: 0.6728 (mt) REVERT: A 88 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.7222 (mmm-85) REVERT: A 112 GLU cc_start: 0.5547 (tt0) cc_final: 0.5310 (tt0) REVERT: A 137 GLU cc_start: 0.6945 (tp30) cc_final: 0.6132 (mm-30) REVERT: B 27 LYS cc_start: 0.7523 (mmmt) cc_final: 0.6918 (mptt) REVERT: D 61 ARG cc_start: 0.7579 (ptt90) cc_final: 0.7034 (mtm180) REVERT: D 74 LYS cc_start: 0.7564 (ptmm) cc_final: 0.7194 (ptmm) REVERT: D 81 GLU cc_start: 0.7591 (pm20) cc_final: 0.7258 (pm20) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.2137 time to fit residues: 20.7834 Evaluate side-chains 77 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 0.0060 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5237 Z= 0.188 Angle : 0.525 6.025 7105 Z= 0.264 Chirality : 0.039 0.194 805 Planarity : 0.005 0.078 848 Dihedral : 11.636 169.214 881 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.68 % Allowed : 15.86 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.35), residues: 623 helix: 2.37 (0.28), residues: 312 sheet: -0.43 (0.50), residues: 108 loop : -1.37 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.014 0.001 PHE A 39 TYR 0.014 0.001 TYR D 49 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6996 (mt) cc_final: 0.6741 (mt) REVERT: A 88 ARG cc_start: 0.7500 (mtp-110) cc_final: 0.7212 (mmm-85) REVERT: A 112 GLU cc_start: 0.5516 (tt0) cc_final: 0.5289 (tt0) REVERT: A 137 GLU cc_start: 0.6956 (tp30) cc_final: 0.6134 (mm-30) REVERT: B 27 LYS cc_start: 0.7516 (mmmt) cc_final: 0.6911 (mptt) REVERT: B 62 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5869 (ttm) REVERT: C 32 TYR cc_start: 0.7779 (m-80) cc_final: 0.7314 (m-80) REVERT: D 61 ARG cc_start: 0.7579 (ptt90) cc_final: 0.7051 (mtm180) REVERT: D 74 LYS cc_start: 0.7556 (ptmm) cc_final: 0.7171 (ptmm) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 0.2447 time to fit residues: 24.0910 Evaluate side-chains 82 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5237 Z= 0.169 Angle : 0.510 5.966 7105 Z= 0.256 Chirality : 0.038 0.191 805 Planarity : 0.005 0.078 848 Dihedral : 10.735 172.745 881 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.68 % Allowed : 15.67 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.35), residues: 623 helix: 2.48 (0.28), residues: 312 sheet: -0.42 (0.50), residues: 108 loop : -1.32 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 PHE 0.014 0.001 PHE A 39 TYR 0.013 0.001 TYR D 49 ARG 0.005 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7781 (tmmt) cc_final: 0.7283 (tptt) REVERT: A 88 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.7225 (mmm-85) REVERT: A 112 GLU cc_start: 0.5438 (tt0) cc_final: 0.5213 (tt0) REVERT: A 137 GLU cc_start: 0.6931 (tp30) cc_final: 0.6148 (mm-30) REVERT: B 27 LYS cc_start: 0.7501 (mmmt) cc_final: 0.6892 (mptt) REVERT: C 32 TYR cc_start: 0.7692 (m-80) cc_final: 0.7220 (m-80) REVERT: D 61 ARG cc_start: 0.7463 (ptt90) cc_final: 0.7139 (mtm180) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.2325 time to fit residues: 23.6020 Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.0060 chunk 7 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5237 Z= 0.175 Angle : 0.522 5.979 7105 Z= 0.263 Chirality : 0.039 0.191 805 Planarity : 0.005 0.078 848 Dihedral : 10.565 175.716 881 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.49 % Allowed : 16.04 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.35), residues: 623 helix: 2.45 (0.28), residues: 318 sheet: -0.37 (0.50), residues: 108 loop : -1.30 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 PHE 0.014 0.001 PHE A 39 TYR 0.014 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7780 (tmmt) cc_final: 0.7279 (tptt) REVERT: A 88 ARG cc_start: 0.7505 (mtp-110) cc_final: 0.7225 (mmm-85) REVERT: A 112 GLU cc_start: 0.5436 (tt0) cc_final: 0.5203 (tt0) REVERT: A 137 GLU cc_start: 0.6931 (tp30) cc_final: 0.6147 (mm-30) REVERT: B 27 LYS cc_start: 0.7507 (mmmt) cc_final: 0.6892 (mptt) REVERT: B 62 MET cc_start: 0.6114 (ttm) cc_final: 0.5913 (ttm) REVERT: C 32 TYR cc_start: 0.7705 (m-80) cc_final: 0.7242 (m-80) REVERT: D 61 ARG cc_start: 0.7472 (ptt90) cc_final: 0.6952 (mtm180) outliers start: 8 outliers final: 8 residues processed: 80 average time/residue: 0.2137 time to fit residues: 21.2886 Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 50 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.174518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142556 restraints weight = 5984.787| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.21 r_work: 0.3633 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5237 Z= 0.199 Angle : 0.536 6.186 7105 Z= 0.270 Chirality : 0.040 0.191 805 Planarity : 0.005 0.077 848 Dihedral : 10.630 177.833 881 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.68 % Allowed : 16.04 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.35), residues: 623 helix: 2.35 (0.28), residues: 318 sheet: -0.40 (0.51), residues: 108 loop : -1.27 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.014 0.001 PHE A 39 TYR 0.015 0.001 TYR D 49 ARG 0.005 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1628.35 seconds wall clock time: 30 minutes 26.91 seconds (1826.91 seconds total)